Thank you for posting the full error message. I assume that you are trying this in your project on PanoramaWeb (although the URL in the error starts with http://localhost:8080...). I see errors in the server log that match the error you posted. I was able to successfully delete the folder referred to in the error message: "Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC". "QC_VelosPro" had been renamed to "Quality Control" earlier today so the actual path was "Dalhousie University - Proteo and Metabolomics Core/Quality Control/QTra5500_QC".

I don't have a good idea for why you got the error. It could be due to the couple of folder rename events that I see in the log. If you have any more folders to delete can you please try to delete them and report back if you get this error again?

Thanks,Vagisha

vagisha responded:

2019-01-08

Hi Alejandro,

This is due to a bug that prevents users from deleting folders. I was able to delete it because I am a site administrator. I will update the server with a fix in the next couple of days and let you know when I am done. Sorry for the inconvenience.

-Vagisha

Alejandro Cohen responded:

2019-01-09

Thanks Vagisha for the quick response.

I'm actually reorganizing the folders because I am adding a new instrument to our QC. After reading the tutorials and webinars, you suggested keeping all instruments as separate folders, is this correct? That's why I only want to keep the folder labeled as Quality Control and its two subfolders. Could you remove the rest until the bug is fixed? (Please delete TEST and Qtrap5500_Metabolomics under our main Dalhousie University Folder).

Thanks!!!

Alex

vsharma responded:

2019-01-09

Hi Alejandro,

In our lab we keep a sub-folder per instrument under a 'QC' folder, similar to the setup you have now. This makes it easy to get a overall view of all the instruments from the dashboard in the parent 'QC' folder.

I deleted TEST and Qtrap5500_Metabolomics folders.

Thanks,Vagisha

Alejandro Cohen responded:

2019-01-18

Hi Vagisha,

I successfully uploaded the previous files via Skyline, but I'm now trying to upload the current files I'm acquiring using AutoQC Uloader. It fails at the very end, this is the log (Below). Any ideas?

I had to restart the PanoramaWeb server around the time there is an error in the log you pasted. That is most likely the cause. Your document did get added to the import queue, however, and got imported successfully on PanoramaWeb. Let me know if you see this problem again.

Thanks,Vagisha

Alejandro Cohen responded:

2019-01-21

Vagisha,

I just checked my Panorama results for this QC, and finally the two files I uploaded via AutoQC Uploader were added to my QC plots, however, there appear to be four points for each peptide precursor for just two files I uploaded.

The file names are: 190118_BSA_QC100_V003_R01 and R02.

Interestingly, the same files appear to have different calculated areas! When I got to the .raw files, I only seem the two files I uploaded.

You are seeing two points per raw file because most of the peptides in your document have two precursors each (+2 and +3). It appears that we are showing one chart per peptide, not one per precursor. The QC summary panel says there are 10 precursors when there are 17. This is a bug - we should have separate plots for each precursor. Thanks for pointing this out!

There are no chromatograms for the +3 precursors from the older raw files. So these precursors must have been added to the Skyline document just before importing the two raw files you mention. Could it have been by accident? I don't see any real signal in most of the +3 chromatograms I looked at.

Thanks,Vagisha

Alejandro Cohen responded:

2019-01-22

Thank you Vagisha,

You are right, I am still curating the Skyline file, removing some precursors with weak signals, unstable or not reproducible precursors (like a few 3+).However, as you mention, the charts should discriminate the different charges for each plot.